Fenneropenaeus chinensis is one of the most important aquaculture species in China. Research on its genomic and genetic structure not only helps us comprehend the genetic basis of complex economic traits, but also offers theoretical guidance in selective breeding. In the present study, a genome survey sequencing was performed to generate a rough reference genome utilized for groping preliminary genome characteristics and facilitate linkage and quantitative trait locus (QTL) mapping. Linkage mapping was conducted using a reduced-representation sequencing method 2b-RAD. In total, 36,762 SNPs were genotyped from 273 progenies in a mapping family, and a high-resolution linkage map was constructed. The consensus map contained 12,884 markers and spanned 5257.81 cM with an average marker interval of 0.41 cM, which was the first high-resolution genetic map in F. chinensis to our knowledge. QTL mapping and association analysis were carried out in 29 characters including body size, sex and disease resistance. 87 significant QTLs were detected in several traits and they were also evaluated by association analysis. Results of this study provide us valuable suggestions in genetic improvement and breeding of new varieties and also lay a basic foundation for further application of cloning of economic genes in selective breeding program and marker-assisted selection.